Hello @Eduardo2000 ,
I have one question , what MBDT version are you using?
There are some rare cases where the GD3000 chip on the DEVKIT-MOTORGD board has some issues with the timing and that why it gets stuck in the GD3000_Config() function.
To fix this we have a new version for that GD3000 Driver, based on The new TPPSDK (GD3000 driver) based on RTD for S32K3 - NXP Community.
I have integrated this driver into the MBDT v1.5.0 release, to use it, you need first to delete all files inside the BLDC and PMSM folders:

Then unzip the attached mc_v1.5.0_tppsdk_rtd_P19.zip archive and paste it in the mc folder

After this you should be able to run the models with no issues, we have been tested this on multiple boards, in multiple regions, with success.
PS: there is a faster way to load the .elf on the S32K344 board, by using MATLAB Command Window:
>> mbd_s32k3.nxp.download.jtag('s32k344_mc_pmsm_2sh_ebt.elf','S32K344')
This will load the pre-generated binary into the S32K344 board, without the need to open the model.
PS2: regarding "Second, every time we press the SW4, the LED D3 goes red indicating a fault I think." this is normal, because SW4 is the Reset button, and LED D3 is the Reset LED for the S32K344 board.
My advice is to press User_SW0 or User_SW1, see below picture:
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Overview of the location of USER_SW0/SW1, RGBLED0, 12 Vin DC power, USB J40 connector, SW1 for powering ON, board jumpers J8, J9, J10, and J11:
PS3: Also please note, that the s32k344_mc_pmsm_2sh_ebt_example_readme.html documentation is updated for all MC models:
The MCSPTE1AK344 Development kit contains:
Let me know how this works,
Stefan V.